fixed merge from development

7 files changed, 52 insertions, 20 deletions

diff --git a/FAQ.md b/FAQ.md
index 2530968..24283cb 100644
--- a/FAQ.md
+++ b/FAQ.md
@@ -1,6 +1,6 @@
-## lazar Frequently Asked Questions
+## *lazar* Frequently Asked Questions
 
-####The LAZAR program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence?
+#### The *lazar* program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence?
 
 In the past many users had problems to interpret the confidence level,
 for this reason we provide now the probabilities that the prediction
@@ -16,3 +16,23 @@ activities of similar compounds.
 Probabilities are calculated from the activities and similarities of
 neighbors, please make sure to inspect the neighbors list for any
 inconsistencies that might affect the prediction.
+
+#### How can I use *lazar* locally on my computer
+If you are familiar with docker, you can use one of our docker images to run lazar locally:
+https://hub.docker.com/r/insilicotox/lazar
+https://hub.docker.com/r/insilicotox/nano-lazar
+
+If you want to install lazar/nano-lazar without docker you should know how to use UNIX/Linux and the Ruby programming language. Source code and brief installation instructions for the GUIs is available at:
+
+https://github.com/opentox/lazar-gui
+https://github.com/opentox/nano-lazar
+
+You can also use just the libraries from the command line:
+
+https://github.com/opentox/lazar
+
+Documentation is available at:
+
+http://www.rubydoc.info/gems/lazar
+
+lazar depends on a couple of external libraries and programs, that could be difficult to install. Due to limited resources we cannot provide support, please use the docker version if you cannot manage it on your own.
diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec
index 2f40224..104fb29 100644
--- a/lazar-gui.gemspec
+++ b/lazar-gui.gemspec
@@ -13,7 +13,7 @@ Gem::Specification.new do |s|
   s.rubyforge_project = "lazar-gui"
   s.files       = `git ls-files`.split("\n")
 
-  s.add_runtime_dependency "lazar", ">= 1.0.0"
+  s.add_runtime_dependency "lazar"
   s.add_runtime_dependency "sinatra"
   s.add_runtime_dependency "rdiscount"
   s.add_runtime_dependency "haml"
diff --git a/qmrf_report.rb b/qmrf_report.rb
index e5fbdf3..a031305 100644
--- a/qmrf_report.rb
+++ b/qmrf_report.rb
@@ -27,24 +27,22 @@ def qmrf_report id
   # Date of QMRF 2.1
   report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
 
-  # QMRF author(s) and contact details 2.1
+  # QMRF author(s) and contact details 2.2
   report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"}
   report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
 
-  if prediction_model.species =~ /TD50/
-    # Date of QMRF update(s) 2.3
-    report.value "qmrf_date_revision", "#{Time.parse("2014-12-05").strftime('%d %B %Y')}"
-    # QMRF update(s) 2.4
-    report.value "qmrf_revision", "Q29-44-39-423"
+  # Date of QMRF update(s) 2.3
+  if prediction_model.name =~ /TD50|multiple/
+    report.value "qmrf_date_revision", "2014-12-05" 
   end
-
-  if prediction_model.species =~ /Rodent/
-    # Date of QMRF update(s) 2.3
-    report.value "qmrf_date_revision", "#{Time.parse("2014-12-05").strftime('%d %B %Y')}"
-    # QMRF update(s) 2.4
-    report.value "qmrf_revision", "Q28-43-38-420"
+ 
+  # Date of QMRF update(s) 2.4
+  if prediction_model.name =~ /TD50/
+    report.value "qmrf_revision", "Q29-44-39-423" 
+  elsif prediction_model.name =~ /multiple/
+    report.value "qmrf_revision", "Q28-43-38-420" 
   end
-
+ 
   # Model developer(s) and contact details 2.5
   report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"}
   report.ref_catalog :model_authors, :authors_catalog, :modelauthor
diff --git a/views/info.haml b/views/info.haml
index 34ded87..d8b93f9 100644
--- a/views/info.haml
+++ b/views/info.haml
@@ -1,2 +1,2 @@
 %div.info
-  currently no models available
+  We are rebuilding the models. It will take a while, please be patient and reload the page in some time.
diff --git a/views/model_details.haml b/views/model_details.haml
index d85d2fb..c5e3370 100644
--- a/views/model_details.haml
+++ b/views/model_details.haml
@@ -28,8 +28,13 @@
     = ", min: #{model.model.algorithms["similarity"]["min"]}"
     %br
     Prediction:
-    %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
-      = model.model.algorithms["prediction"]["method"]
+    - if model.model.algorithms["prediction"]["method"] !~ /Caret/
+      %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+        = model.model.algorithms["prediction"]["method"]
+    - else
+      %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox/Algorithm/Caret", :rel=>"external"}
+        = model.model.algorithms["prediction"]["method"]
+
     %br
     Descriptors:
     = model.model.algorithms["descriptors"]["method"]+","
diff --git a/views/predict.haml b/views/predict.haml
index 89bef7c..2308911 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -180,5 +180,6 @@
         %h2
           3. Predict
       %div.col-lg-10.col-md-10.col-sm-10.col-xs-10
-        %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "getsmiles()"}
+        %button.has-feedback.btn.btn-warning.h2{:type => "submit", :id => "submit", :value=>"", :onclick => "getsmiles()"}
+          %span.glyphicon.glyphicon-play
         %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index bb7c631..8c4af6f 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -1,3 +1,11 @@
+:javascript
+  $(document).ready(function(){
+    $('[data-toggle="popover"]').popover();
+    $('.modal').on('hidden.bs.modal', function () {
+      $(this).removeData('bs.modal');
+    });
+  });
+
 %div.well
   %a.btn.btn-warning{:href => to('/predict')}
     %i.glyphicon.glyphicon-menu-left